Contacts of the helix formed by residues 113 - 134 (chain A) in PDB entry 6Z1V
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A GLY* 1.3 78.4 - - - +
114A LYS* 1.3 65.8 + - - +
115A ASP* 3.4 8.8 + - - +
116A GLU* 2.8 40.5 + - - +
117A VAL* 3.0 19.5 + - - +
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER* 1.3 72.5 - - - +
115A ASP* 1.3 82.9 + - - +
117A VAL* 3.2 7.8 + - - +
118A ILE* 3.0 41.4 + - + +
189A PHE* 4.1 24.8 - - + +
190A ASP* 3.2 31.0 + - - +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER* 3.2 7.3 + - - +
114A LYS* 1.3 103.5 + - - +
116A GLU* 1.3 57.2 + - + +
118A ILE* 3.4 13.5 + - - +
119A LYS* 3.0 29.5 + - - +
186A LYS* 3.9 12.1 + - - +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY* 3.2 13.0 - - - -
113A SER* 2.8 46.0 + - - +
115A ASP* 1.3 76.5 - - + +
117A VAL* 1.3 57.8 + - - +
119A LYS* 3.4 7.0 + - - +
120A GLU* 3.0 37.9 + - + +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY 4.0 19.5 - - - +
113A SER 3.0 14.9 + - - +
114A LYS* 3.6 9.2 - - - +
116A GLU* 1.3 74.4 - - - +
118A ILE* 1.3 67.3 + - - +
120A GLU* 3.2 7.2 + - + +
121A VAL* 3.1 30.2 + - + +
189A PHE* 4.1 26.5 - - + -
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LYS* 3.0 26.9 + - + +
115A ASP* 3.7 14.8 - - - +
117A VAL* 1.3 75.9 - - - +
119A LYS* 1.3 63.4 + - - +
121A VAL* 3.2 2.3 + - - +
122A GLN* 2.9 53.2 + - + +
185A ILE* 4.0 2.4 - - + +
186A LYS* 3.7 43.7 - - + +
189A PHE* 3.5 46.0 - - + -
190A ASP* 4.1 8.7 - - - +
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP 3.0 17.7 + - - +
116A GLU* 3.7 7.6 - - - +
118A ILE* 1.3 77.7 - - - +
120A GLU* 1.3 60.7 + - - +
122A GLN* 3.3 14.1 + - - +
123A GLU* 2.9 39.5 + - + +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 3.0 25.3 + - + +
117A VAL* 3.2 7.2 + - + +
119A LYS* 1.3 78.5 - - - +
121A VAL* 1.3 61.3 + - + +
123A GLU* 3.4 5.1 + - - +
124A PHE* 2.9 24.4 + - - +
301A PGE 3.2 30.5 + - - +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 3.1 26.9 + - + +
118A ILE* 5.0 0.4 - - - -
120A GLU* 1.3 74.8 - - + +
122A GLN* 1.3 66.4 + - - +
124A PHE* 3.3 11.6 + - + +
125A TYR* 2.9 22.2 + - + +
146A ILE* 6.2 3.6 - - + -
185A ILE* 3.6 34.1 - - + -
189A PHE* 5.1 8.1 - - + -
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Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 2.9 38.6 + - - +
119A LYS* 3.6 13.9 - - - +
121A VAL* 1.3 77.2 - - - +
123A GLU* 1.3 57.8 + - + +
125A TYR* 3.2 4.3 + - - +
126A LYS* 3.0 40.4 + - - +
182A PRO* 2.9 45.6 + - + +
183A ASP* 5.7 0.4 + - - -
185A ILE* 3.9 16.4 - - + -
186A LYS* 4.0 9.7 - - - +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS* 2.9 24.0 + - + +
120A GLU* 3.9 8.1 - - - +
122A GLN* 1.3 74.8 - - + +
124A PHE* 1.3 66.9 + - - +
126A LYS* 3.3 26.8 + - - +
127A ASP* 2.9 38.9 + - - +
301A PGE 4.0 17.7 - - - -
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLU 2.9 18.4 + - - +
121A VAL* 3.5 13.2 - - + +
123A GLU* 1.3 77.0 - - - +
125A TYR* 1.3 66.8 + - + +
127A ASP* 3.4 0.7 + - - +
128A THR* 2.8 43.7 + - - -
142A THR* 4.0 27.8 - - + -
146A ILE* 4.3 14.8 - - + -
301A PGE 3.5 54.2 + - - +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A VAL 2.9 13.4 + - - +
122A GLN* 3.2 8.3 + - - +
124A PHE* 1.3 81.7 - - + +
126A LYS* 1.3 59.3 + - - +
128A THR* 3.2 3.2 + - - -
129A TYR* 2.8 45.7 + + - +
143A LEU* 3.4 26.0 - - + -
146A ILE* 4.1 20.4 - - + -
147A HIS* 2.7 32.7 + + - -
154A GLY* 3.0 27.0 + - - -
155A LEU* 3.8 20.2 - - + -
163A ILE* 3.9 0.5 - - - +
181A CYS* 3.6 32.8 - - + -
182A PRO* 4.1 5.2 - - + -
185A ILE* 3.9 12.6 - - + -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLN* 3.0 25.6 + - - +
123A GLU* 3.9 27.8 + - - +
125A TYR* 1.3 77.9 - - - +
127A ASP* 1.3 66.3 + - - +
129A TYR* 3.4 5.3 + - - +
130A ASN* 3.0 33.9 + - - +
155A LEU* 4.0 24.5 - - + -
182A PRO* 3.9 26.8 - - + +
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 2.9 26.5 + - - +
124A PHE 3.9 0.9 - - - +
126A LYS* 1.3 78.2 - - - +
128A THR* 1.3 57.9 + - - +
130A ASN* 3.3 11.0 + - - +
131A LYS* 3.0 34.8 + - - +
301A PGE 2.9 50.0 - - - +
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 2.8 32.8 + - + -
125A TYR* 3.7 3.1 - - - -
127A ASP* 1.3 73.2 - - - +
129A TYR* 1.3 66.4 + - - +
131A LYS* 3.2 5.8 + - - +
132A LEU* 3.0 22.9 + - - +
139A GLN* 3.4 30.6 - - + +
142A THR* 4.7 9.0 - - + -
143A LEU* 3.6 26.5 - - + -
301A PGE 3.0 24.2 + - - +
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Residues in contact with TYR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 2.8 39.4 + + + +
126A LYS* 3.5 5.8 - - - +
128A THR* 1.3 77.5 - - - +
130A ASN* 1.3 76.7 + - - +
132A LEU* 3.3 3.5 + - - +
133A LYS* 3.0 23.6 + - + +
143A LEU* 4.0 10.2 - - - +
154A GLY* 3.8 17.7 - - - -
155A LEU* 3.6 27.0 + - + -
158A GLY 4.9 0.7 + - - -
160A GLU* 2.5 45.2 + - - +
162A PHE* 3.6 18.2 - + - -
163A ILE* 3.6 31.2 - - + -
101B ARG* 3.5 6.6 + - - -
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Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LYS* 3.0 27.5 + - - +
127A ASP* 3.8 11.0 + - - +
129A TYR* 1.3 89.4 - - - +
131A LYS* 1.3 65.3 + - + +
133A LYS* 3.2 15.4 + - + +
134A THR* 3.2 27.7 + - + +
155A LEU* 5.1 3.8 - - - +
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP* 3.0 20.9 + - - +
128A THR* 3.2 7.2 + - - +
130A ASN* 1.3 76.4 - - + +
132A LEU* 1.3 62.5 + - - +
134A THR* 2.8 24.2 + - - -
136A ASP* 3.2 23.9 + - + +
139A GLN* 3.9 28.6 - - + +
301A PGE 3.7 36.0 + - - -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A THR 3.0 12.6 + - - +
129A TYR 3.7 7.4 - - - +
131A LYS* 1.3 76.5 - - - +
133A LYS* 1.3 58.2 + - - +
135A LYS* 2.8 19.6 + - - -
136A ASP* 3.6 21.1 - - - +
137A GLU* 3.6 28.7 - - - +
139A GLN* 4.3 4.2 - - + +
140A ARG* 3.7 43.5 + - + +
143A LEU* 3.7 24.5 - - + -
162A PHE* 3.9 20.9 - - + -
163A ILE* 4.3 9.4 - - + -
166A ILE* 4.3 0.4 - - + -
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 3.0 16.1 + - + +
130A ASN* 3.4 17.0 + - - +
131A LYS 3.2 0.2 - - - -
132A LEU* 1.3 75.8 - - - +
134A THR* 1.3 60.6 + - + +
135A LYS* 3.6 1.9 + - - +
160A GLU* 3.1 34.5 + - - +
162A PHE* 3.5 39.8 - - + +
101B ARG* 5.8 0.6 - - - +
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Residues in contact with THR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASN* 3.2 13.7 + - + +
131A LYS* 2.8 22.1 + - - -
133A LYS* 1.3 81.0 - - + +
135A LYS* 1.3 68.0 + - - +
136A ASP* 3.7 2.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il